Both of these Xml are same, it does not matter if prefix is used or not as good as Xml elements belong to the namespace as per defined scheme. Its not a valid requirement to request xml with specific prefix. Even if you need to do it, use custom Xslt.

Out of desperation, I started deploying the pipeline over and over again, leaving off different components each time until I tracked down the culprit. As it turns out, my local development VM (and Visual Studio) pulled one of the components out of the GAC rather than the standard C:\Program Files...